Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000375.1 Kokia drynarioides strain JFW-HI SEQ_111166, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 123102
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:14029 original size:17 final size:16
Alignment explanation
Indices: 14003--14036 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13993 TTTTTTTTAC
14003 TATTACAAATAAAATA
1 TATTACAAATAAAATA
*
14019 TATTCACAAATATAATA
1 TATT-ACAAATAAAATA
14036 T
1 T
14037 TAATACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTACAAATAAAATA
Found at i:22829 original size:14 final size:14
Alignment explanation
Indices: 22812--22898 Score: 68
Period size: 14 Copynumber: 5.8 Consensus size: 14
22802 TTTTCAGTTA
*
22812 TTTTATTTTTCTAT
1 TTTTATTTTTATAT
*
22826 TTTTATTTTTATTT
1 TTTTATTTTTATAT
22840 TTTTATAATTTATATAT
1 TTTTAT--TTT-TATAT
22857 TGTTCTGAATTTTTATAT
1 T-TT-T--ATTTTTATAT
* *
22875 ATTTATTTTCAT-T
1 TTTTATTTTTATAT
22888 TTTTATTTTTA
1 TTTTATTTTTA
22899 ATGTATATAC
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
13 10 0.17
14 25 0.42
16 4 0.07
17 7 0.12
18 7 0.12
19 4 0.07
21 2 0.03
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTATTTTTATAT
Found at i:23707 original size:2 final size:2
Alignment explanation
Indices: 23700--23733 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23690 TAAAATTAAC
23700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23734 TTAAATATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24335 original size:18 final size:19
Alignment explanation
Indices: 24304--24339 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24294 GATTCAATGT
*
24304 TTTTTTTCTCTGATTTACC
1 TTTTTTTATCTGATTTACC
24323 TTTTTTTAT-TGATTTAC
1 TTTTTTTATCTGATTTAC
24340 AGTGCTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTTTTATCTGATTTACC
Found at i:27585 original size:19 final size:20
Alignment explanation
Indices: 27542--27591 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
27532 CTTAATATTC
*
27542 TATTTGATATTTAATTTTAA
1 TATTTAATATTTAATTTTAA
*
27562 T-TTTAATATTTAA-TTTAG
1 TATTTAATATTTAATTTTAA
*
27580 TATTTAAAATTT
1 TATTTAATATTT
27592 TCAATTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTAATATTTAATTTTAA
Found at i:29086 original size:142 final size:144
Alignment explanation
Indices: 28931--29188 Score: 371
Period size: 143 Copynumber: 1.8 Consensus size: 144
28921 AAACAATAAT
* * * ** *
28931 AATTAAATTTATTTAGTTAAATTATGCTATTAGTCATGTA-TTTGTTTAAGGTTATAAATTTAAT
1 AATTAAATCTATTTAGTTAAATTATGCTACTAGTCATGTACTATGCGTAAAGTTATAAATTTAAT
28995 CCAT-ATTCTTCAATTTGATCATTCATAG-CTCTTATACTTTTC-AAATTTTAAAATTTTAATCT
66 CCATAATT-TTCAATTTGATCATTCATAGTC-CTTATACTTTTCAAAATTTTAAAATTTTAATCT
29057 TGATCCAAATGATAGC
129 TGATCCAAATGATAGC
* * *
29073 AATTAAATCTATTTGGTTAAATTCTGCTACTAGTCTTGTACTATGCGTAAAGTTATAAATTTAAT
1 AATTAAATCTATTTAGTTAAATTATGCTACTAGTCATGTACTATGCGTAAAGTTATAAATTTAAT
**
29138 CCATAATTTTCAATTTGATCATTTTTAGTCCTTATACTTTTCAAAATTTTA
66 CCATAATTTTCAATTTGATCATTCATAGTCCTTATACTTTTCAAAATTTTA
29189 TTTTGATGCA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
142 35 0.35
143 54 0.53
144 12 0.12
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (144 bp):
AATTAAATCTATTTAGTTAAATTATGCTACTAGTCATGTACTATGCGTAAAGTTATAAATTTAAT
CCATAATTTTCAATTTGATCATTCATAGTCCTTATACTTTTCAAAATTTTAAAATTTTAATCTTG
ATCCAAATGATAGC
Found at i:40258 original size:251 final size:247
Alignment explanation
Indices: 39809--40582 Score: 765
Period size: 251 Copynumber: 3.1 Consensus size: 247
39799 ATCCTTCTAC
* * * *
39809 AAACTGAATTCATTTCACCTT-AA-AGTATCTCCATTATCATCAGCAAAATCCCATTTATGTTTT
1 AAACTGAATTCATTTCACCTTAAAGAGTGTCACCATTATCATCAACAAAA-CCCATTTCT-TTTT
* * *
39872 TCAGTATTCTCAGCACAACTATTTAG-TATTTACTACCAAATGAATAAAAATTGAAAAAAAAATA
64 TCAGGATTCTC-G-AC-AC-----AGCTATTTACTACCAAATGAATAAAAATTG-AAAAATATTA
* * * * * *
39936 T-TATCAAACAATCAGACATATTTATCACTCAACTAAACAAGATTAAAAACACTGAATCCTTTAG
120 TCAAACAGACAATAAGACATATTTAT-ACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAG
* * * *
40000 GAAATGAAGAACCATGTTCATTAAAAATGAATATAAAATTCTTCTGCAAACATAAA-AGTTCCTG
184 AAAATGAAGAACAATGTTCATAAAAAATGAATATAAAATCCTTCTGCAAACA-AAATAGTTCCTG
*
40064 AAACTGAATTCATTTCACCTTAAAGCAGTGTCACCATTATCATCATCAAAACCCATTTCTTTTTT
1 AAACTGAATTCATTTCACCTTAAAG-AGTGTCACCATTATCATCAACAAAACCCATTTCTTTTTT
*
40129 CAGGATTCTCGACACAGCTATTTACTACCGAATGAATAAAAATTGAAAATATGATTATCAAACAG
65 CAGGATTCTCGACACAGCTATTTACTACCAAATGAATAAAAATTGAAAA-AT-ATTATCAAACAG
* * *
40194 ACAATAAGACACATTTACTACTCAGTTAAACAAGATTTAAAACACTGAATTCTTTAGAAAATGAA
128 ACAATAAGACATATTTA-TACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAA
* * * * *
40259 GAAGAATGTT--TGAAAAAATGGATATAAAATCCTTTTGCTAACAAAATAGTTGCTG
192 GAACAATGTTCAT-AAAAAATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTG
* * * *
40314 AAACTTAATTCATTTCACATTAAAGTAGTGTCACCATTATCATAAGAAAATAACACCATTTCTTT
1 AAACTGAATTCATTTCACCTTAAAG-AGTGTCACCATTATCATCA-ACAA-AAC-CCATTTCTTT
* * *
40379 TTTCATGG-TTCTC-A-ACAACTATTTCCTACCAAATGAAT-AAAATATGAAACTAAATATGATC
62 TTTCA-GGATTCTCGACACAGCTATTTACTACCAAATGAATAAAAAT-TG-AA--AAATATTATC
* * * *
40440 AAAC-G---ATCAAG-CATA-TTAAACTCAGCTGAACAAGATTAAAAACACTG-TTTCTAATAGA
122 AAACAGACAAT-AAGACATATTTATACTCAGCTAAACAAGATTAAAAACACTGAATTCT-TTAGA
* * ** *
40498 AAATGAAGAACAATGTTCATAAAAAATGTATATAACATCCAGCTGCAAACAAAATAGATCCTG
185 AAATGAAGAACAATGTTCATAAAAAATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTG
40561 AGAACTGAATTCATTTCACCTT
1 A-AACTGAATTCATTTCACCTT
40583 GAATTAGTGT
Statistics
Matches: 442, Mismatches: 54, Indels: 53
0.81 0.10 0.10
Matches are distributed among these distances:
245 4 0.01
246 45 0.10
247 39 0.09
248 30 0.07
249 34 0.08
250 83 0.19
251 93 0.21
252 16 0.04
253 24 0.05
254 6 0.01
255 22 0.05
256 16 0.04
257 8 0.02
258 22 0.05
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (247 bp):
AAACTGAATTCATTTCACCTTAAAGAGTGTCACCATTATCATCAACAAAACCCATTTCTTTTTTC
AGGATTCTCGACACAGCTATTTACTACCAAATGAATAAAAATTGAAAAATATTATCAAACAGACA
ATAAGACATATTTATACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAAGAAC
AATGTTCATAAAAAATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTG
Found at i:58872 original size:29 final size:30
Alignment explanation
Indices: 58829--58885 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
58819 AAATTAGATC
*
58829 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
*
58859 AAATC-AAAGTTCATGTATACAATTACA
1 AAATCAAAAGTTCATGTATAAAATTACA
58886 TAGTAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:67215 original size:4 final size:4
Alignment explanation
Indices: 67206--67230 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
67196 ATTGTCTATA
67206 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
67231 CCCTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:67287 original size:33 final size:33
Alignment explanation
Indices: 67249--67315 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
67239 AAAGCCTCTT
67249 TACGCCTCAAATAATTAGATCAAACCTCATTAA
1 TACGCCTCAAATAATTAGATCAAACCTCATTAA
67282 TACGCCTCAAATAATTAGATCAAACCTCATTAA
1 TACGCCTCAAATAATTAGATCAAACCTCATTAA
67315 T
1 T
67316 CTTTCTTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (33 bp):
TACGCCTCAAATAATTAGATCAAACCTCATTAA
Found at i:69105 original size:19 final size:19
Alignment explanation
Indices: 69081--69120 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
69071 CACTGAATTG
69081 AATATTGAAATTAAAT-TTA
1 AATATT-AAATTAAATATTA
*
69100 AATATTAAATTGAATATTA
1 AATATTAAATTAAATATTA
69119 AA
1 AA
69121 ATAAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AATATTAAATTAAATATTA
Found at i:69136 original size:31 final size:31
Alignment explanation
Indices: 69076--69150 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
69066 ACTAACACTG
* * *
69076 AATTGAATATTGAAATTAAATTTAAATATTA
1 AATTGAATATTAAAATAAAATTCAAATATTA
* *
69107 AATTGAATATTAAAATAAAATTCAGATATTG
1 AATTGAATATTAAAATAAAATTCAAATATTA
* *
69138 AGTTGTATATTAA
1 AATTGAATATTAA
69151 CCCAGAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (31 bp):
AATTGAATATTAAAATAAAATTCAAATATTA
Found at i:73059 original size:30 final size:30
Alignment explanation
Indices: 73015--73101 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
73005 ATCGACCGCA
* *
73015 GGGAGAAACCAAGGAAAAGCACCGATGCCC
1 GGGAAAAACCAAGGAAAAGCACCGATACCC
* *
73045 GGGACAAGCCAAGGAAAAGCACCGATACCC
1 GGGAAAAACCAAGGAAAAGCACCGATACCC
*
73075 GGGAAAAACCAAGGAAAAGCATCGATA
1 GGGAAAAACCAAGGAAAAGCACCGATA
73102 GGCCTGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.44, C:0.24, G:0.28, T:0.05
Consensus pattern (30 bp):
GGGAAAAACCAAGGAAAAGCACCGATACCC
Found at i:79989 original size:37 final size:37
Alignment explanation
Indices: 79942--80015 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
79932 CATCGAAAGA
*
79942 AAGTCTAATTAGAGGGTGCCTATAAGCGCCATTTAAG
1 AAGTCTAATTAGAGGGTGCCTATAAACGCCATTTAAG
79979 AAGTCTAATTAGAGGGTGCCTATAAACGCCATTTAAG
1 AAGTCTAATTAGAGGGTGCCTATAAACGCCATTTAAG
80016 TCTTAAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (37 bp):
AAGTCTAATTAGAGGGTGCCTATAAACGCCATTTAAG
Found at i:97701 original size:92 final size:92
Alignment explanation
Indices: 97544--97729 Score: 354
Period size: 92 Copynumber: 2.0 Consensus size: 92
97534 ACCAAAGGAA
*
97544 TGTGAGATGATTAAGTGGTAGCATACTTGCCCATTGGTGTCGTATAAGAGGATAGGTTCAAACCC
1 TGTGAGATGATTAAGTGGTAGCATACTTGCCCATCGGTGTCGTATAAGAGGATAGGTTCAAACCC
97609 TACAAAGTGTGAATGCTCAGGTCTCCT
66 TACAAAGTGTGAATGCTCAGGTCTCCT
*
97636 TGTGAGATGATTAAGTGGTAGCATACTTGCCCATCGGTGTCGTATAAGAGTATAGGTTCAAACCC
1 TGTGAGATGATTAAGTGGTAGCATACTTGCCCATCGGTGTCGTATAAGAGGATAGGTTCAAACCC
97701 TACAAAGTGTGAATGCTCAGGTCTCCT
66 TACAAAGTGTGAATGCTCAGGTCTCCT
97728 TG
1 TG
97730 GTAGGTGGTA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (92 bp):
TGTGAGATGATTAAGTGGTAGCATACTTGCCCATCGGTGTCGTATAAGAGGATAGGTTCAAACCC
TACAAAGTGTGAATGCTCAGGTCTCCT
Found at i:106158 original size:2 final size:2
Alignment explanation
Indices: 106151--106178 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
106141 AAAATTTTAA
106151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106179 CAAAAGATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106358 original size:6 final size:6
Alignment explanation
Indices: 106347--106373 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
106337 TTATTCGAAG
106347 AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
106374 TCCAAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:114738 original size:23 final size:23
Alignment explanation
Indices: 114712--114757 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
114702 TTTTTTCATA
* *
114712 TTTTATTTACT-ATTTTCTGTTT
1 TTTTTTTTACTAATTTTCTATTT
*
114734 TTTTTTTTCCTAATTTTCTATTT
1 TTTTTTTTACTAATTTTCTATTT
114757 T
1 T
114758 GAACCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTTTTTACTAATTTTCTATTT
Found at i:115238 original size:57 final size:57
Alignment explanation
Indices: 115150--115276 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
115140 TTATTAGTTT
115150 TTTTTTTTGTCATTCAACTTTAAAAAATTACAAAATA-TTCTTTTAACCATTCAATTA
1 TTTTTTTTGTCATTCAACTTTAAAAAATTACAAAATACTT-TTTTAACCATTCAATTA
* * *
115207 TTTTTTTTGTCATTCAATTTTAAAAAATTACAAATTACTTTTTTAACCATTCAATTG
1 TTTTTTTTGTCATTCAACTTTAAAAAATTACAAAATACTTTTTTAACCATTCAATTA
115264 TCTTTTTTTGTCA
1 T-TTTTTTTGTCA
115277 GCATAGTCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
57 52 0.80
58 13 0.20
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTTTTTTGTCATTCAACTTTAAAAAATTACAAAATACTTTTTTAACCATTCAATTA
Found at i:122936 original size:23 final size:24
Alignment explanation
Indices: 122901--122945 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
122891 TTAATCCCTA
*
122901 TATTCTAATTTGTTTAATTTTAGT
1 TATTCTAATTTGTTGAATTTTAGT
*
122925 TATTGTAA-TTGTTGAATTTTA
1 TATTCTAATTTGTTGAATTTTA
122946 AAATTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (24 bp):
TATTCTAATTTGTTGAATTTTAGT
Done.